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RNA-SEQ on resting (R) and stimulated (S) B cells from several IgH 3'RR mutant models

ABSTRACT: We evaluated by RNA-seq obveral transcripts in B cells (resting and activated for 2 days with LPS) sorted from several KO mice models devoid of portion or all the IgH 3' Regulatory Region

ORGANISM(S): Mus musculus

PROVIDER: GSE76217 | GEO | 2016/03/02

SECONDARY ACCESSION(S): PRJNA306658

REPOSITORIES: GEO

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RNA-SEQ on resting (R) and stimulated (S) B cells from several IgH 3'RR mutant models

Project description:We evaluated by RNA-seq obveral transcripts in B cells (resting and activated for 2 days with LPS) sorted from several KO mice models devoid of portion or all the IgH 3' Regulatory Region One RNA-seq point was realized per condition (resting or stimulated) and per genotype. Each point corresponds to a pool of equivalent number of B cells sorted from 4 animals

2016-03-02 | E-GEOD-76217 | biostudies-arrayexpress

HDAC inhibitors and IgH locus transcription. Mini 3'RR and IgH locus transcription

Project description:Numerous B-cell lymphomas feature translocations linking oncogenes with the IgH locus and epigenetic drugs such as histone deacetylase inhibitors (HDACi) have been approved to treat some of them. In this study we investigated IgH locus transcription in B-cell splenocytes stimulated with LPS and the HDACi SAHA. B-cell development is spatially and temporally regulated with the 3'RR enhancer of the IgH locus as a conductor. 3'RR is composed of 4 enhancer elements with a palindromic structure of great significance. We investigated the role of this palindrome with KOKI mice where the 30Kb structure of the 3'RR has been deleted of its palindromic structure.

2021-03-27 | GSE169690 | GEO

SmallRNA-SEQ of mutants B cell for IgH 3'RR and Emu

Project description:SmallRNA-SEQ of mutants B cell for IgH 3'RR and Emu

2017-06-13 | GSE90759 | GEO

RNA-SEQ of mutants B cell for IgH 3'RR and Emu

Project description:RNA-SEQ of mutants B cell for IgH 3'RR and Emu

2017-06-13 | GSE90758 | GEO

5C Chromatin interactions in the Igh locus in resting splenic B cells

Project description:5C Chromatin interactions in the Igh locus in resting splenic B cells

| PRJNA761346 | ENA

HDAC inhibitors and IgH locus transcription. Mini 3'RR and IgH locus transcription

Project description:HDAC inhibitors and IgH locus transcription. Mini 3'RR and IgH locus transcription

| PRJNA717674 | ENA

5C Chromatin interactions in the Igh locus in resting splenic B cells

Project description:These tracks include chromatin interaction data produced using the 5C (chromatin conformation capture carbon copy) method by the Kenter Lab located at the University of Illinois College of Medicine, Chicago, IL. These tracks show looping interactions across the Igh locus using alternating forward and reverse primer design scheme. The 3C method uses formaldehyde crosslinking to covalently associate interacting chromatin segments in intact cells. The cells are then lysed and chromatin is digested with the Hind III restriction enzyme. The digested fragments are ligated under dilute conditions to promote intra-molecular ligation. A genome-wide interaction library of ligation products corresponding to all possible chromatin interactions is produced by this method. In 5C assays, over 12,000 potential ligation products specific to the Igh locus are detected by PCR using multiplexed primer pairs. Here we focused on the 3’ end of the Igh locus to evaluate the status of the constant region domain of the locus in LPS+IL4 activated splenic B cells. We observe that the configuration of the 3’ end of the Igh locus spanning the CH region genes assumes a developmental stage specific configuration in B lineage B cells. We find that the interaction frequency and activation state of the 3’ enhancer increases as B cells mature.

2021-11-23 | GSE183574 | GEO

Transcriptome analysis of B cell lymphomas in several c-myc Igh transgenic mice

Project description:Investigation of B cell lymphomas (IgM+ IgD+) located in various places (lung, mesenteric lymph nodes,…) of three different c-myc Igh transgenic mice. Insertion of c-myc in 5' to Emu (cr), in 5' to Cmu with Emu deletion (hv), and in Calpha (co).

2020-01-21 | GSE132721 | GEO

Expression data for resting and activated B and T cells

Project description:The IgH locus encodes for part of the antibody exposed by B cells and is important for the immune system. In B cells, one allele produces protein, the other must remain silenced. It was proposed that both alleles reside in different nuclear compartments and that this is important to maintain mono-allelic productivity. Here we challenge this concept. We provide detailed genome-wide contact maps, which show that IgH adopts different nuclear locations in immune versus other cells but also demonstrate that in B cells both alleles reside in the same environment. Nuclear positioning is therefore not important to maintain allelic exclusion. We did a gene expression analysis on resting (Day 0) and in vitro activated (Day 4) B and T cells in triplicate Splenic B cells and T cells were separately isolated from spleen, using magnetic activated cell sorting, and activated in vitro for 4 days

2013-06-01 | E-GEOD-46865 | biostudies-arrayexpress

Deep sequencing of the murine Igh repertoire reveals complex regulation of non-random V gene rearrangement frequencies

Project description:A diverse antibody repertoire is formed through the rearrangement of V, D, and J segments at the immunoglobulin heavy chain (Igh) loci. The C57BL/6 murine Igh locus has over 100 functional VH gene segments that can recombine to a rearranged DJH. While the non-random usage of VH genes is well documented, it is not clear what elements determine recombination frequency. To answer this question we conducted deep sequencing of 5M-bM-^@M-^Y-RACE products of the Igh repertoire in pro-B cells, amplified in an unbiased manner. ChIP-seq results for several histone modifications and RNA polymerase II binding, RNA-seq for sense and antisense non-coding germline transcripts, and proximity to CTCF and Rad21 sites were compared to the usage of individual V genes. Computational analyses assessed the relative importance of these various accessibility elements. These elements divide the Igh locus into four epigenetically and transcriptionally distinct domains, and our computational analyses reveal different regulatory mechanisms for each region. Proximal V genes are relatively devoid of active histone marks and non-coding RNA in general, but having a CTCF site near their RSS is critical, suggesting that position near the base of the chromatin loops is important for rearrangement. In contrast, distal V genes have high levels of histone marks and non-coding RNA, which may compensate for their poorer RSS and for being distant from CTCF sites. Thus, the Igh locus has evolved a complex system for the regulation of V(D)J rearrangement that is different for of each the four domains that comprise this locus. For the ChIP-seq, input and immunoprecipitated DNA was given to The Scripps DNA Array Facility, where it was prepared for massively parallel sequencing on Illumina HiSeq2000.

2013-08-05 | E-GEOD-47766 | biostudies-arrayexpress

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